Mercurial > repos > devteam > fasta_concatenate_by_species
annotate fasta_concatenate_by_species.xml @ 1:d9f0a11824e9
Add bx-python dependency (for maf_utilities.py).
| author | Nate Coraor <nate@bx.psu.edu> |
|---|---|
| date | Mon, 17 Nov 2014 10:08:37 -0500 |
| parents | a63b082a26eb |
| children | c5311b7718d1 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fasta_concatenate0" name="Concatenate" version="0.0.0"> |
| 2 <description>FASTA alignment by species</description> | |
|
1
d9f0a11824e9
Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
parents:
0
diff
changeset
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3 <requirements> |
|
d9f0a11824e9
Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
parents:
0
diff
changeset
|
4 <requirement type="package" version="0.7.1">bx-python</requirement> |
|
d9f0a11824e9
Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
parents:
0
diff
changeset
|
5 </requirements> |
| 0 | 6 <command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command> |
| 7 <inputs> | |
| 8 <param name="input1" type="data" format="fasta" label="FASTA alignment"/> | |
| 9 </inputs> | |
| 10 <outputs> | |
| 11 <data name="out_file1" format="fasta"/> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input1" value="cf_maf2fasta.dat" /> | |
| 16 <output name="out_file1" file="fasta_concatenate_out.fasta" /> | |
| 17 </test> | |
| 18 </tests> | |
| 19 <help> | |
| 20 | |
| 21 **What it does** | |
| 22 | |
| 23 This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment. | |
| 24 It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species. | |
| 25 | |
| 26 ------- | |
| 27 | |
| 28 **Example** | |
| 29 | |
| 30 Starting FASTA:: | |
| 31 | |
| 32 >hg18.chr1(+):10016339-10016341|hg18_0 | |
| 33 GT | |
| 34 >panTro2.chr1(+):10195380-10195382|panTro2_0 | |
| 35 GT | |
| 36 >rheMac2.chr1(+):13119747-13119749|rheMac2_0 | |
| 37 GT | |
| 38 >mm8.chr4(-):148269679-148269681|mm8_0 | |
| 39 GT | |
| 40 >canFam2.chr5(+):66213635-66213637|canFam2_0 | |
| 41 GT | |
| 42 | |
| 43 >hg18.chr1(-):100323677-100323679|hg18_1 | |
| 44 GT | |
| 45 >panTro2.chr1(-):101678671-101678673|panTro2_1 | |
| 46 GT | |
| 47 >rheMac2.chr1(-):103154011-103154013|rheMac2_1 | |
| 48 GT | |
| 49 >mm8.chr3(+):116620616-116620618|mm8_1 | |
| 50 GT | |
| 51 >canFam2.chr6(+):52954092-52954094|canFam2_1 | |
| 52 GT | |
| 53 | |
| 54 | |
| 55 | |
| 56 becomes:: | |
| 57 | |
| 58 >hg18 | |
| 59 GTGT | |
| 60 >panTro2 | |
| 61 GTGT | |
| 62 >rheMac2 | |
| 63 GTGT | |
| 64 >mm8 | |
| 65 GTGT | |
| 66 >canFam2 | |
| 67 GTGT | |
| 68 | |
| 69 | |
| 70 .. class:: warningmark | |
| 71 | |
| 72 This tool will only work properly on files with Galaxy style FASTA headers. | |
| 73 | |
| 74 </help> | |
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1
d9f0a11824e9
Add bx-python dependency (for maf_utilities.py).
Nate Coraor <nate@bx.psu.edu>
parents:
0
diff
changeset
|
75 </tool> |